Later on Thursday, shareholders voted in favour of the re-election of Murdoch's son James as chairman.
Just 51.6% backed Murdoch to stay in the top job.
Only 36% supported the company's remuneration report.
Sky confirmed in its annual report last month that chief executive Jeremy Darroch's total annual pay packet more than trebled to £16.3m (€18.1m) past year despite annual profits being hit by the cost of broadcasting live Premier League football. About £12m came from a long term incentive scheme, but he also received an nearly maximum annual bonus of £1.9m.
"There's nothing wrong with Mr Murdoch - but it is because of the name".
Some investor groups had expressed unease over him serving longer, in light of James being also chief executive of 21st Century Fox - which is seeking to buy the 61 percent of Sky it does not already own.
Today, Sky noted that if 21st Century Fox's offer is not approved by the CMA by the end of the year, a special dividend of 10p per Sky share will be paid to shareholders in February 2018.
In response, Martin Gilbert, Sky's deputy chairman, pointed out that Sky's board had formed an independent committee to evaluate the terms of 21st Century Fox's takeover, which he said had met 11 times since the takeover approach was tabled in December a year ago.
The deal has been referred to the Competition and Markets Authority (CMA) by Karen Bradley, Secretary of State for Culture, Media and Sport, on concerns over media plurality and broadcasting standards.
Regulators on Tuesday said the probe would assess Rupert Murdoch's influence on Britain's political landscape. He also refused to comment on whether Fox was getting a "sweetheart deal" on the price it will pay for Sky.
The shareholder, Hugh Lawson, said: "I think the board lacks independence. Even though I wasn't talented he put me in charge".
Sky CEO Jeremy Darroch, Fox CFO John Nallen and former Fox no. 2 Chase Carey were also among those board members re-elected on Thursday, each with more than 98.5 percent of the shareholder vote in their favor.
Martin Gilbert, the deputy chair, said the board had looked at the Fox takeover in the best interests of shareholders and had impartial discussions that did not include Murdoch or other Sky directors with connections to Fox.